I believe it will. I am putting in a 2000 motor as we speak. But it is necessary for me to use the 2000 harness and ECU too because of the coil change (Luckily mine came with it all). You can do the harness and ECU from the yj, but it will require splicing from hell, and there will be many things (like your gauges and other things) that wont work right because the run off you computer. Best thing to do is get a 97 to 99 harness.

By the way, I think my 4.0 might be a little more torquey, but thats because its a stroker.

will the 97-99 harness work on the 95 motor/trans/case? splicing wires wont be an issue i can do that in my sleep, but if the TJ harness will make it more plug and play then ill go that route, Ive been w/o my jeep since June 4th, I'm ready to drive it again

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I bought a couple things from them, they have just about everything but I think they are expensive. You may want to shop around a little bit.

Some things seem expensive, some dont. I got my entire engine/tranny swap from them last year for 1200. That was wiring,computer, engine, auto trans, shifter and all cables, transfer case input shaft, and whatever else I needed. It was from a 99 with 60,000 mi. It doesn't hurt to call

It would probably be easier to get a TJ harness and ECM. Should be plug and play that way.

I've never done a fuel injected engine swap using OEM harness's and ECM's.

Put an LSX engine into a 69 Camaro last year. Used Accel DFI and a painless wiring harness. Kinda like it better that way, since with the DFI if you change cams, add turbos/superchargers ect... you can program it yourself. But thats a totally different story then what you're doing.

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1990 2.5 YJ / 1997 2.5 TJ

USAF VET

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And most of the sensors on the yj's engine ran off 9 volts, tj's were mostly 5 volts if I remember correctly, so you might be having to replace some sending units and other sensors off the engine, transmission, etc.